Current methods of molecular barcoding and sequence analysis are typically limited to the 3′end of the target transcript, because molecular barcodes were attached to the 3′ end, and Illumina sequencing length is short. Molecular barcoding of sequences upstream of transcript 3′end can be performed using gene-specific reverse transcription (RT) primers, the scalability is limited because RT primer with large amounts of molecular barcodes are designed against each gene, making it expensive to manufacture barcoded primers in a large gene pool. Methods for long read sequencing are limited by high sequencing error rates, low read throughput, and absence of molecular barcoding, which are aspects that prevent accurate sequence analysis, quantification, and lack of scalability.